In the past few decades, growing adoption of electronic health records (EHRs) systems have made massive clinical narrative data available electronically. Natural language processing (NLP) technologies that can unlock information from narrative text have received great attention in the medical domain. Many clinical NLP methods and systems have been developed and showed promising results in various information extraction tasks. These methods and tools have also been successfully applied to facilitate clinical research, as well as to support healthcare applications. At the same time, the availability and use of health information online has exploded through use of social media, question-answering and community discussion forums, and health-related websites. These present additional challenges and opportunities for further development of new methodologies and healthcare applications.

The goal of this workshop is to provide a unique platform to bring together researchers and practitioners in healthcare informatics working with health-related free text, and facilitate close interaction among students, scholars, and industry professionals on health NLP challenges worldwide. This is a one-day workshop that consists of invited speakers, podium talks, and poster presentations. The workshop will be held on June 10th, 2019, at Beijing, China, in conjunction with the IEEE International Conference on Healthcare Informatics (ICHI 2019).

We invite papers and short abstracts on novel approaches, works in progress, comparative analyses of tools, and original state-of-the-art work in health NLP methods, tools, and applications. Selected papers will be presented as podium talks, and other interesting submissions and abstracts will be showcased as poster presentations.



Target audience includes both health NLP researchers and consumers. Anyone interested in NLP-based approaches, solutions, and applications in clinical, biomedical, and consumer health informatics is welcome. Researchers and students working on health NLP projects and others interested in learning about and sharing NLP knowledge and resources are strongly encouraged to attend. We also welcome students who wish to closely interact with NLP experts. Potential attendees may come from NLP communities in the medical domain (e.g., AMIA NLP Working Group, BioNLP) and computer and information scientists and linguists working on health-related text processing (e.g., with interests in ACL, EMNLP, NAACL, TREC Precision Medicine and Clinical Decision Support tracks, etc.), as well as general health informatics professionals and researchers.


Time Title Speaker
2:00 - 2:10pm Welcome to HealthNLP Hua Xu, The University of Texas Health Science Center at Houston
2:10 - 2:30pm Information Extraction for Populating Lung Cancer Clinical Research Data Hongfang Liu, Mayo Clinic
2:30 - 2:50pm RCorp:an Resource for Chemical Disease Semantic Extraction in Chinese Jiao Li, Institute of Medical Information, Chinese Academy of Medical Sciences
2:50 - 3:10pm A Study of Deep Learning Methods for De-identification of Clinical Notes at Cross Institute Settings Jiang Bian, University of Florida
3:10 - 3:30pm TestIME: Testing Chinese Input Method Engines in the Electronic Medical Record Entry Task Feihong Yang, Institute of Medical Information and Library, Chinese Academy of Medical Sciences
3:30 - 4:00pm Coffee Break
4:00 - 4:20pm Applying a Deep Learning-Based Sequence Labeling Approach to Detect Attributes of Medical Concepts in Clinical Text Hua Xu, The University of Texas Health Science Center at Houston
4:20 - 4:40pm A Hybrid Semantic Relatedness Algorithm by Entity Co-Occurrence and Specialized Word Embeddings Go Eun Heo, Yonsei University
4:40 - 5:00pm Using the WHO database of spontaneous reports to build joint vector representations of drugs and adverse drug reactions, a promising avenue for pharmacovigilance Lucie M. Gattepaille, Uppsala Monitoring Centre Uppsala, Sweden
5:00 - 5:20pm Combined Attention Mechanism for Named Entity Recognition in Chinese Electronic Medical Records Li Hou, Institute of Medical Information, Chinese Academy of Medical Science
5:20 - 5:40pm Improving Rare Disease Classification Using Imperfect Knowledge Graph Qiaozhu Mei, University of Michigan

Important dates

  • Deadline for all submissions: March 25th, 2019 Extended to March 28th, 2019
  • Notification of decisions: April 15th, 2019
  • Deadline for camera-ready papers: May 3rd, 2019
  • Workshop date: June 10th, 2019

Submission and Review

Authors may submit regular papers (4-10 pages, including references) and abstracts (2 pages, including references) in the format used for the ICHI submissions. Developers of NLP tools may submit a demo paper (up to 4 pages, including references) describing the tool, along with a link to a web demonstration (interactive website or a demonstration video). As with ICHI, the workshop will follow single-blind reviewing, therefore submissions should have the names and affiliations of authors listed on the paper. Papers must adhere to the IEEE Proceedings Format available for LaTeX and Word, and submitted as a single PDF file. Submissions will be handled electronically through EasyChair ( For more information, please read the detailed submission instructions (link here).

All submissions will undergo a peer review by at least two domain experts from the program committee. The selection of papers and posters will be primarily based on the potential to generate discussion and impact future research directions. Accepted papers will be included in the ICHI 2019 Proceedings and IEEE Digital Library. Selected papers will be invited to publish an extended version of their work in a special issue of BMC Medical Informatics and Decision Making journal with a discount publication fee.



  • Hua Xu, PhD (contact), Professor, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, US. email
  • Ozlem Uzuner, PhD, Associate Professor, Information Sciences and Technology, George Mason University, Fairfax, VA, US. email
  • Yanshan Wang, PhD, Research Associate, Biomedical Informatics, Mayo Clinic, Rochester, MN, US. email

Steering committee:

  • Wendy Chapman, PhD, Professor and Chair, Department of Biomedical Informatics, University of Utah, Salt Lake City, US. email
  • Dina Demner Fushman, MD, PhD, Scientist, Lister Hill Center, National Library of Medicine, US. email
  • Hongfang Liu, Professor, Biomedical Informatics, Mayo Clinic, Rochester, MN, US. email
  • Stephane Meystre, MD, PhD, Chair and Founding Director, Translational Biomedical Informatics Center, Associate Professor, Psychiatry Department and Biomedical Informatics Center, Medical University of South Carolina, US. email
  • Guergana Savova, PhD, Associate Professor, Harvard Medical School and Children’s Hospital Boston, Boston, MA, US. email
  • Buzhou Tang, PhD, Associate Professor, Department of Computer Science, Harbin Institute of Technology, Shenzhen, China. email
  • Karin Verspoor, PhD, Professor, School of Computing and Information Systems and Deputy Director of the Health and Biomedical Informatics Centre, University of Melbourne, Australia email
  • Pierre Zweigenbaum, PhD, Head of LIMSI, French National Centre for Scientific Research, Paris, France, email

More to be updated...